Caffe script to compute accuracy and confusion matrix

convnet_test.py

#!/usr/bin/python
# -*- coding: utf-8 -*-

# Author: Axel Angel, copyright 2015, license GPLv3.

import sys
import caffe
import numpy as np
import lmdb
import argparse
from collections import defaultdict

def flat_shape(x):
    "Returns x without singleton dimension, eg: (1,28,28) -> (28,28)"
    return x.reshape(filter(lambda s: s > 1, x.shape))

def lmdb_reader(fpath):
    import lmdb
    lmdb_env = lmdb.open(fpath)
    lmdb_txn = lmdb_env.begin()
    lmdb_cursor = lmdb_txn.cursor()

    for key, value in lmdb_cursor:
        datum = caffe.proto.caffe_pb2.Datum()
        datum.ParseFromString(value)
        label = int(datum.label)
        image = caffe.io.datum_to_array(datum).astype(np.uint8)
        yield (key, flat_shape(image), label)

def leveldb_reader(fpath):
    import leveldb
    db = leveldb.LevelDB(fpath)

    for key, value in db.RangeIter():
        datum = caffe.proto.caffe_pb2.Datum()
        datum.ParseFromString(value)
        label = int(datum.label)
        image = caffe.io.datum_to_array(datum).astype(np.uint8)
        yield (key, flat_shape(image), label)

def npz_reader(fpath):
    npz = np.load(fpath)

    xs = npz['arr_0']
    ls = npz['arr_1']

    for i, (x, l) in enumerate(np.array([ xs, ls ]).T):
        yield (i, x, l)

if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('--proto', type=str, required=True)
    parser.add_argument('--model', type=str, required=True)
    group = parser.add_mutually_exclusive_group(required=True)
    group.add_argument('--lmdb', type=str, default=None)
    group.add_argument('--leveldb', type=str, default=None)
    group.add_argument('--npz', type=str, default=None)
    args = parser.parse_args()

    count = 0
    correct = 0
    matrix = defaultdict(int) # (real,pred) -> int
    labels_set = set()

    net = caffe.Net(args.proto, args.model, caffe.TEST)
    caffe.set_mode_cpu()
    print "args", vars(args)
    if args.lmdb != None:
        reader = lmdb_reader(args.lmdb)
    if args.leveldb != None:
        reader = leveldb_reader(args.leveldb)
    if args.npz != None:
        reader = npz_reader(args.npz)

    for i, image, label in reader:
        image_caffe = image.reshape(1, *image.shape)
        out = net.forward_all(data=np.asarray([ image_caffe ]))
        plabel = int(out['prob'][0].argmax(axis=0))

        count += 1
        iscorrect = label == plabel
        correct += (1 if iscorrect else 0)
        matrix[(label, plabel)] += 1
        labels_set.update([label, plabel])

        if not iscorrect:
            print("\rError: i=%s, expected %i but predicted %i" \
                    % (i, label, plabel))

        sys.stdout.write("\rAccuracy: %.1f%%" % (100.*correct/count))
        sys.stdout.flush()

    print(", %i/%i corrects" % (correct, count))

    print ""
    print "Confusion matrix:"
    print "(r , p) | count"
    for l in labels_set:
        for pl in labels_set:
            print "(%i , %i) | %i" % (l, pl, matrix[(l,pl)])

HI,

Where is flat_shape defined?

same question !

File "convnet_test.py", line 24, in lmdb_reader
yield (key, flat_shape(image), label)
NameError: global name 'flat_shape' is not defined

try my modified script if you dont use the lmdb but use the training images txt file.
https://gist.github.com/stardust2602/79c818add4f7100397dd

How to use it for hdf5 files?? Pls help

I've added flat_shape, it's just to remove empty dimensions.

If you implement it, I'll happily update the gist above. Try something along the lines:

import h5py
def hdf5_reader(file_name):
 file = h5py.File(file_name, 'r') # open read-only
 group_name = file.keys[0] # try to find the first group
 group = file[group_name]
 for key, value in dict(group).iteritems():
        datum = caffe.proto.caffe_pb2.Datum()
        datum.ParseFromString(value)
        label = int(datum.label)
        image = caffe.io.datum_to_array(datum).astype(np.uint8)
        yield key, flat_shape(image), label

To cope with encoded images I extended the code above like this:

def getImage(datum):
    if datum.encoded:
        from cStringIO import StringIO
        import PIL
        s = StringIO(datum.data)
        image = np.array(PIL.Image.open(s))
    else:
        image = caffe.io.datum_to_array(datum).astype(np.uint8)
    return image


def lmdb_reader(fpath):
    lmdb_env = lmdb.open(fpath)
    lmdb_txn = lmdb_env.begin()
    lmdb_cursor = lmdb_txn.cursor()

    for key, value in lmdb_cursor:
        datum = caffe.proto.caffe_pb2.Datum()
        datum.ParseFromString(value)
        label = int(datum.label)
        image = getImage(datum)
        yield (key, flat_shape(image), label)


def leveldb_reader(fpath):
    import leveldb
    db = leveldb.LevelDB(fpath)

    for key, value in db.RangeIter():
        datum = caffe.proto.caffe_pb2.Datum()
        datum.ParseFromString(value)
        label = int(datum.label)
        image = getImage(datum)
        yield (key, flat_shape(image), label)

@axel-angel, Don't you need to subtract the image mean like in the example here: https://github.com/BVLC/caffe/blob/7003d1b8e24416cb5bdb5537a7805cb5a9de2ca1/examples/00-classification.ipynb
Also what about channel swap?

@alex-angel, In addition images would need channel swap as well correct?

I am working on LMDB database. when I am running this code I am getting convnet_test.py: error: argument --proto is required error. Please help.

@monjoybme You need launch like this:
python ../src/convnet_test_lmdb.py --proto lenet.prototxt --model snapshots/lenet_mnist_v3-id_iter_1000.caffemodel --lmdb ../caffe/examples/mnist/mnist_test_lmdb/

accord @axel-angel

Regards

@axel-angle, thanks for your amazing work.
I am using your script and I got stuck at:

I1119 17:07:53.463573 12920 net.cpp:283] Network initialization done.
args{'proto': 'test.prototxt', 'model': 'models/caffenet_age_train_iter_50000.caffemodel', 'lmdb': 'lmdb_full/age_test_lmdb/', 'leveldb': None, 'npz': None}
Traceback (most recent call last):
  File "convnet_test.py", line 75, in <module>
    for i, image, label in reader:
  File "convnet_test.py", line 28, in lmdb_reader
    yield (key, flat_shape(image), label)
  File "convnet_test.py", line 15, in flat_shape
    return x.reshape(filter(lambda s: s > 1, x.shape))
TypeError: expected sequence object with len >= 0 or a single integer

I used python3 to run. Can u suggest me a solution? Thanks.